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How can I map sRNAs (20-30nt) to a reference, knowing that there are gaps in the sRNA?
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BBMap should be able to handle that without much trouble; it allows gaps in very short reads. How long do you expect the gaps to be? -
I guess also hundreds of nt compared to the reference, but it's just a speculation.. thanksComment
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If you expect them to be hundreds of nt (which seems unlikely to me... normally small RNA introns, if present, are very short) you can try this:
bbmap.sh ref=ref.fa in=reads.fq out=mapped.sam maxindel=500 tipsearch=500 k=11 slow
The slow flag, longer-than-default tipsearch, and most importantly shorter-than-default k will greatly slow it down (particularly on a large genome), but should ensure that you capture all the introns in those very short reads. Be sure to adapter-trim them prior to mapping.Comment
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